Objective. The purpose of this study was to determine the fecal level of zonulin, tumor necrosis factor alpha (TNFα) and nitric oxide metabolites in children with gastrointestinal forms of food allergy (FA) and to assess their pathogenetic significance in the diagnosis of IgE-dependent and IgE-independent FA. Methods. It was clinical and laboratory examines 39 children with food allergy to the cow milk protein at the age of 6 months to 3 years (Group I). The comparison group (Group II) consisted of 30 healthy children. The content of zonulin was determined using Immunodiagnostic (Germany) reagents using enzyme-linked immunosorbent assay (ELISA). Immunological study of fecal TNFα was performed with the help of BSM (USA) reagents using the enzyme-linked immunosorbent assay (ELISA) method. The concentration of NO metabolites in co-filters was determined using an enzyme immunoassay (ELISA) and the “Total Nitric Oxide and Nitrate/Nitrite Parameter Assay Kit” (R&D Systems, USA). Results. Mean concentrations of zonulin in fecal samples in FA children and in control group children were 1.79±0.16 and 0.75±0.01 ng/ml, respectively (p<0.05). The level of TNFα (31,04±2,71 mmol/L) in FA children was in 7.6 times higher than in the control group. Analyze of the NO metabolites content in children with IgE-dependent and IgE-independent FA show the multidirectional changes in production of nitric oxide in children of different subgroups. Conclusions. Determination of fecal zonuline concentrations, TNFα and NO metabolites is an informative criterion for damage of the intestinal barrier in the development of food allergies in children. High numbers of these fecal markers are characteristic of the IgE-dependent form of the disease, increased zonulin, TNFα and decreased NO metabolites are characteristic of IgE-independent FA in children.